CBS-domain / CBS-domain / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta Similarity search - Domain/homology
Type: MARMOSAIC 325 mm CCD / Detector: CCD / Date: May 27, 2008 / Details: Flat mirror (vertical focusing)
Radiation
Monochromator: Single crystal Si(111) bent monochromator (horizontal focusing) Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
Relative weight: 1
Reflection
Resolution: 1.8→29.617 Å / Num. obs: 28983 / % possible obs: 99.1 % / Observed criterion σ(I): -3 / Biso Wilson estimate: 24.648 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 17.67
Reflection shell
Diffraction-ID: 1
Resolution (Å)
Highest resolution (Å)
Rmerge(I) obs
Mean I/σ(I) obs
Num. measured obs
Num. unique obs
% possible all
1.8-1.86
0.529
2.5
17350
4948
93.2
1.86-1.94
0.372
3.8
23077
6070
99.4
1.94-2.03
0.264
5.4
21827
5724
99.5
2.03-2.13
0.169
8.2
20249
5289
99.6
2.13-2.27
0.116
11.4
22873
5955
99.7
2.27-2.44
0.085
15
21232
5521
99.9
2.44-2.69
0.063
19.3
22331
5794
99.8
2.69-3.07
0.043
26.7
21356
5528
99.7
3.07-3.87
0.028
37.6
22222
5745
99.9
3.87
0.023
45.3
22172
5708
99.7
-
Phasing
Phasing
Method: SAD
-
Processing
Software
Name
Version
Classification
NB
REFMAC
5.2.0019
refinement
PHENIX
refinement
SHELX
phasing
MolProbity
3beta29
modelbuilding
XSCALE
datascaling
PDB_EXTRACT
3.004
dataextraction
XDS
datareduction
SHELXD
AUTOSHARP
phasing
Refinement
Method to determine structure: SAD / Resolution: 1.8→29.617 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.948 / SU B: 4.781 / SU ML: 0.077 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.118 / ESU R Free: 0.115 Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE ...Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. A MET-INHIBITION PROTOCOL WAS USED FOR SELENOMETHIONINE INCORPORATION DURING PROTEIN EXPRESSION. THE OCCUPANCY OF THE SE ATOMS IN THE MSE RESIDUES WAS REDUCED TO 0.75 FOR THE REDUCED SCATTERING POWER DUE TO PARTIAL S-MET INCORPORATION. 3. ATOM RECORDS CONTAIN RESIDUAL B FACTORS ONLY. 4. PEG (PEG600) IS PRESENT IN CRYSTALLIZATION CONDITION. 5. AMP WAS MODELED BASED ON DENSITY AND STRUCTURAL HOMOLOGS.
Rfactor
Num. reflection
% reflection
Selection details
Rfree
0.206
1469
5.1 %
RANDOM
Rwork
0.168
-
-
-
obs
0.17
28971
99.27 %
-
Solvent computation
Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parameters
Biso mean: 21.676 Å2
Baniso -1
Baniso -2
Baniso -3
1-
-0.79 Å2
0 Å2
-0.98 Å2
2-
-
1.87 Å2
0 Å2
3-
-
-
-1.2 Å2
Refinement step
Cycle: LAST / Resolution: 1.8→29.617 Å
Protein
Nucleic acid
Ligand
Solvent
Total
Num. atoms
2183
0
30
283
2496
Refine LS restraints
Refine-ID
Type
Dev ideal
Dev ideal target
Number
X-RAY DIFFRACTION
r_bond_refined_d
0.015
0.022
2306
X-RAY DIFFRACTION
r_bond_other_d
0.001
0.02
1553
X-RAY DIFFRACTION
r_angle_refined_deg
1.509
2.001
3141
X-RAY DIFFRACTION
r_angle_other_deg
0.97
3
3837
X-RAY DIFFRACTION
r_dihedral_angle_1_deg
5.671
5
296
X-RAY DIFFRACTION
r_dihedral_angle_2_deg
34.593
24.565
92
X-RAY DIFFRACTION
r_dihedral_angle_3_deg
13.295
15
434
X-RAY DIFFRACTION
r_dihedral_angle_4_deg
19.712
15
14
X-RAY DIFFRACTION
r_chiral_restr
0.082
0.2
389
X-RAY DIFFRACTION
r_gen_planes_refined
0.005
0.02
2486
X-RAY DIFFRACTION
r_gen_planes_other
0.001
0.02
431
X-RAY DIFFRACTION
r_nbd_refined
0.204
0.2
481
X-RAY DIFFRACTION
r_nbd_other
0.19
0.2
1699
X-RAY DIFFRACTION
r_nbtor_refined
0.172
0.2
1161
X-RAY DIFFRACTION
r_nbtor_other
0.087
0.2
1198
X-RAY DIFFRACTION
r_xyhbond_nbd_refined
0.169
0.2
204
X-RAY DIFFRACTION
r_symmetry_vdw_refined
0.239
0.2
11
X-RAY DIFFRACTION
r_symmetry_vdw_other
0.218
0.2
31
X-RAY DIFFRACTION
r_symmetry_hbond_refined
0.142
0.2
21
X-RAY DIFFRACTION
r_mcbond_it
2.259
3
1550
X-RAY DIFFRACTION
r_mcbond_other
0.545
3
571
X-RAY DIFFRACTION
r_mcangle_it
2.995
5
2335
X-RAY DIFFRACTION
r_scbond_it
4.807
8
957
X-RAY DIFFRACTION
r_scangle_it
6.626
11
796
LS refinement shell
Resolution: 1.8→1.847 Å / Total num. of bins used: 20
Rfactor
Num. reflection
% reflection
Rfree
0.277
101
-
Rwork
0.226
1889
-
all
-
1990
-
obs
-
-
93.03 %
Refinement TLS params.
Method: refined / Origin x: 8.5137 Å / Origin y: 20.2633 Å / Origin z: -20.4589 Å
11
12
13
21
22
23
31
32
33
T
-0.0468 Å2
0.0168 Å2
0.0047 Å2
-
-0.0597 Å2
-0.0052 Å2
-
-
-0.0518 Å2
L
1.231 °2
0.0239 °2
0.485 °2
-
0.2227 °2
0.0421 °2
-
-
1.1451 °2
S
-0.0185 Å °
0.0173 Å °
0.0387 Å °
-0.0145 Å °
0.0117 Å °
0.0189 Å °
-0.0289 Å °
0.0025 Å °
0.0068 Å °
+
About Yorodumi
-
News
-
Feb 9, 2022. New format data for meta-information of EMDB entries
New format data for meta-information of EMDB entries
Version 3 of the EMDB header file is now the official format.
The previous official version 1.9 will be removed from the archive.
In the structure databanks used in Yorodumi, some data are registered as the other names, "COVID-19 virus" and "2019-nCoV". Here are the details of the virus and the list of structure data.
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)
EMDB accession codes are about to change! (news from PDBe EMDB page)
The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
The EM Navigator/Yorodumi systems omit the EMD- prefix.
Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator
Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.
Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi